The Genomics Workbench within BIONODE is a comprehensive, browser-based suite for analysing sequencing data, with every tool presented as a simple web form that runs on the IBDC compute backend. There is nothing to install and no command line to learn. The toolset spans the full path from raw reads to results, covering quality control, read cleaning, genome alignment, alignment processing, variant calling, gene-expression analysis, and the file and annotation utilities that support them.
It is built for both newcomers and experienced researchers: quick one-step jobs sit alongside complete pipelines such as DNA variant calling from raw reads to a filtered VCF. Below is the list of tools available in Genomics Workbench version 1.0, followed by the tools currently in beta testing and releasing soon.
Curated list of commonly used genomics tools with primary references
| # | Tool | Reference / Link |
|---|---|---|
| 1 | MultiQC | https://multiqc.info/ |
| 2 | FastQC | https://www.bioinformatics.babraham.ac.uk/projects/fastqc/ |
| 3 | fastp | Chen et al. (2018) |
| 4 | Trimmomatic | Bolger et al. (2014) |
| 5 | Bowtie 2 | Langmead & Salzberg (2012) |
| 6 | BWA-MEM2 | Vasimuddin et al. (2019) |
| 7 | Minimap2 | Li (2018) |
| 8 | STAR | Dobin et al. (2013) |
| 9 | GATK | De Summa et al. (2017) |
| 10 | BCFtools | Danecek & McCarthy (2017) |
| 11 | SnpEff | Cingolani et al. (2012) |
| 12 | ANNOVAR | Wang et al. (2010) |
| 13 | SAMtools | Li et al. (2009) |
| 14 | SPAdes | Bankevich et al. (2012) |
| 15 | Canu | Koren et al. (2017) |
| 16 | Flye | Kolmogorov et al. (2019) |
| 17 | BUSCO | Waterhouse et al. (2018) |
| 18 | IGV | Thorvaldsdóttir et al. (2013) |
| 19 | DESeq2 | Love et al. (2014) |
| 20 | edgeR | Robinson et al. (2010) |